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Histone H3 lysine 27 methylation asymmetry on developmentally-regulated promoters distinguish the first two lineages in mouse preimplantation embryos.

Dahl JA, Reiner AH, Klungland A, Wakayama T, Collas P - PLoS ONE (2010)

Bottom Line: The majority of H3K4/K27me3 co-enriched promoters are distinct between the two lineages, primarily due to differences in the distribution of H3K27me3.Derivation of embryonic stem cells leads to significant losses and gains of H3K4/K27me3 co-enriched promoters relative to the ICM, with distinct contributions of (de)methylation events on K4 and K27.Our results show histone trimethylation asymmetry on promoters in the first two developmental lineages, and highlight an epigenetic skewing associated with embryonic stem cell derivation.

View Article: PubMed Central - PubMed

Affiliation: Institute of Basic Medical Sciences, University of Oslo and Norwegian Center for Stem Cell Research, Oslo, Norway.

ABSTRACT
First lineage specification in the mammalian embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to embryonic and extraembryonic tissues. We show here that this first differentiation event is accompanied by asymmetric distribution of trimethylated histone H3 lysine 27 (H3K27me3) on promoters of signaling and developmentally-regulated genes in the mouse ICM and TE. A genome-wide survey of promoter occupancy by H3K4me3 and H3K27me3 indicates that both compartments harbor promoters enriched in either modification, and promoters co-enriched in trimethylated H3K4 and H3K27 linked to developmental and signaling functions. The majority of H3K4/K27me3 co-enriched promoters are distinct between the two lineages, primarily due to differences in the distribution of H3K27me3. Derivation of embryonic stem cells leads to significant losses and gains of H3K4/K27me3 co-enriched promoters relative to the ICM, with distinct contributions of (de)methylation events on K4 and K27. Our results show histone trimethylation asymmetry on promoters in the first two developmental lineages, and highlight an epigenetic skewing associated with embryonic stem cell derivation.

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Distribution of H3K4me3, H3K27me3 and H3K4/K27me3 promoters in the ICM and TE.(A) Isolation of ICMs (white arrow) and TEs (black arrow) from E4 blastocysts by microdissection (left panels), followed by immunosurgery of the ICM/TE halves to purify the ICM (large arrow). (B) 2-D scatter plots of averaged MaxTen values for H3K4me3 vs. H3K27me3 log2 signal intensities in the ICM (left) and TE (right). Data points were colored to indicate classification according to the peak calling algorithm to show H3K4me3-enriched promoters (green), H3K27me3-enriched promoters (red) and promoters co-enriched in H3K4me3 and H3K27me3 (blue). (C) H3K4me3 and H3K27me3 enrichment profiles on indicated promoters in the ICM and TE. Data are expressed as log2 ChIP/Input ratios. (D) Venn diagram analysis of H3K4me3 and H3K27me3 promoters in ICM and TE. (E) Average distribution of H3K4me3 and H3K27me3 on H3K4/K27me3, H3K4me3 and H3K27me3 promoters, relative to the position of the TSS (red bar).
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pone-0009150-g001: Distribution of H3K4me3, H3K27me3 and H3K4/K27me3 promoters in the ICM and TE.(A) Isolation of ICMs (white arrow) and TEs (black arrow) from E4 blastocysts by microdissection (left panels), followed by immunosurgery of the ICM/TE halves to purify the ICM (large arrow). (B) 2-D scatter plots of averaged MaxTen values for H3K4me3 vs. H3K27me3 log2 signal intensities in the ICM (left) and TE (right). Data points were colored to indicate classification according to the peak calling algorithm to show H3K4me3-enriched promoters (green), H3K27me3-enriched promoters (red) and promoters co-enriched in H3K4me3 and H3K27me3 (blue). (C) H3K4me3 and H3K27me3 enrichment profiles on indicated promoters in the ICM and TE. Data are expressed as log2 ChIP/Input ratios. (D) Venn diagram analysis of H3K4me3 and H3K27me3 promoters in ICM and TE. (E) Average distribution of H3K4me3 and H3K27me3 on H3K4/K27me3, H3K4me3 and H3K27me3 promoters, relative to the position of the TSS (red bar).

Mentions: Mouse blastocysts cultured in vitro from the two-cell stage contain >60 cells, including ∼20 in the ICM and the rest in the TE. We purified TEs by bisection and ICMs by dissection followed by immunosurgery (Figure 1A). Isolated ICMs and TEs were viable because they reformed new blastocysts and trophoblastic vesicles, respectively (Figure S1). ICM and TE chromatin was subjected to triplicate H3K4me3 and H3K27me3 µChIPs and ChIP DNA was hybridized to microarrays tiling −2 to +0.5 kb relative to the transcription start site (TSS) of ∼27,000 promoters, including 19,489 RefSeq promoters. Reproducibility of µChIP-chip relative to Q2ChIP-chip (from 100,000 cells) and between µChIP-chip replicates has previously been reported [23]. Reproducibility was further shown here by two-dimensional scatter plots of MaxTen values for H3K4me3 and H3K27me3 (Figure S2A,B), and by the similarity of average enrichment profiles on metagenes (Figure S2C) and of promoter-specific enrichment patterns (Figure S2D and Figure S3).


Histone H3 lysine 27 methylation asymmetry on developmentally-regulated promoters distinguish the first two lineages in mouse preimplantation embryos.

Dahl JA, Reiner AH, Klungland A, Wakayama T, Collas P - PLoS ONE (2010)

Distribution of H3K4me3, H3K27me3 and H3K4/K27me3 promoters in the ICM and TE.(A) Isolation of ICMs (white arrow) and TEs (black arrow) from E4 blastocysts by microdissection (left panels), followed by immunosurgery of the ICM/TE halves to purify the ICM (large arrow). (B) 2-D scatter plots of averaged MaxTen values for H3K4me3 vs. H3K27me3 log2 signal intensities in the ICM (left) and TE (right). Data points were colored to indicate classification according to the peak calling algorithm to show H3K4me3-enriched promoters (green), H3K27me3-enriched promoters (red) and promoters co-enriched in H3K4me3 and H3K27me3 (blue). (C) H3K4me3 and H3K27me3 enrichment profiles on indicated promoters in the ICM and TE. Data are expressed as log2 ChIP/Input ratios. (D) Venn diagram analysis of H3K4me3 and H3K27me3 promoters in ICM and TE. (E) Average distribution of H3K4me3 and H3K27me3 on H3K4/K27me3, H3K4me3 and H3K27me3 promoters, relative to the position of the TSS (red bar).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2818844&req=5

pone-0009150-g001: Distribution of H3K4me3, H3K27me3 and H3K4/K27me3 promoters in the ICM and TE.(A) Isolation of ICMs (white arrow) and TEs (black arrow) from E4 blastocysts by microdissection (left panels), followed by immunosurgery of the ICM/TE halves to purify the ICM (large arrow). (B) 2-D scatter plots of averaged MaxTen values for H3K4me3 vs. H3K27me3 log2 signal intensities in the ICM (left) and TE (right). Data points were colored to indicate classification according to the peak calling algorithm to show H3K4me3-enriched promoters (green), H3K27me3-enriched promoters (red) and promoters co-enriched in H3K4me3 and H3K27me3 (blue). (C) H3K4me3 and H3K27me3 enrichment profiles on indicated promoters in the ICM and TE. Data are expressed as log2 ChIP/Input ratios. (D) Venn diagram analysis of H3K4me3 and H3K27me3 promoters in ICM and TE. (E) Average distribution of H3K4me3 and H3K27me3 on H3K4/K27me3, H3K4me3 and H3K27me3 promoters, relative to the position of the TSS (red bar).
Mentions: Mouse blastocysts cultured in vitro from the two-cell stage contain >60 cells, including ∼20 in the ICM and the rest in the TE. We purified TEs by bisection and ICMs by dissection followed by immunosurgery (Figure 1A). Isolated ICMs and TEs were viable because they reformed new blastocysts and trophoblastic vesicles, respectively (Figure S1). ICM and TE chromatin was subjected to triplicate H3K4me3 and H3K27me3 µChIPs and ChIP DNA was hybridized to microarrays tiling −2 to +0.5 kb relative to the transcription start site (TSS) of ∼27,000 promoters, including 19,489 RefSeq promoters. Reproducibility of µChIP-chip relative to Q2ChIP-chip (from 100,000 cells) and between µChIP-chip replicates has previously been reported [23]. Reproducibility was further shown here by two-dimensional scatter plots of MaxTen values for H3K4me3 and H3K27me3 (Figure S2A,B), and by the similarity of average enrichment profiles on metagenes (Figure S2C) and of promoter-specific enrichment patterns (Figure S2D and Figure S3).

Bottom Line: The majority of H3K4/K27me3 co-enriched promoters are distinct between the two lineages, primarily due to differences in the distribution of H3K27me3.Derivation of embryonic stem cells leads to significant losses and gains of H3K4/K27me3 co-enriched promoters relative to the ICM, with distinct contributions of (de)methylation events on K4 and K27.Our results show histone trimethylation asymmetry on promoters in the first two developmental lineages, and highlight an epigenetic skewing associated with embryonic stem cell derivation.

View Article: PubMed Central - PubMed

Affiliation: Institute of Basic Medical Sciences, University of Oslo and Norwegian Center for Stem Cell Research, Oslo, Norway.

ABSTRACT
First lineage specification in the mammalian embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to embryonic and extraembryonic tissues. We show here that this first differentiation event is accompanied by asymmetric distribution of trimethylated histone H3 lysine 27 (H3K27me3) on promoters of signaling and developmentally-regulated genes in the mouse ICM and TE. A genome-wide survey of promoter occupancy by H3K4me3 and H3K27me3 indicates that both compartments harbor promoters enriched in either modification, and promoters co-enriched in trimethylated H3K4 and H3K27 linked to developmental and signaling functions. The majority of H3K4/K27me3 co-enriched promoters are distinct between the two lineages, primarily due to differences in the distribution of H3K27me3. Derivation of embryonic stem cells leads to significant losses and gains of H3K4/K27me3 co-enriched promoters relative to the ICM, with distinct contributions of (de)methylation events on K4 and K27. Our results show histone trimethylation asymmetry on promoters in the first two developmental lineages, and highlight an epigenetic skewing associated with embryonic stem cell derivation.

Show MeSH